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4 TCA/PDH/HPM/Uronic
Acid Pathway
[BIOCHEM] 2.4 TCA/PDH/HPM/Uronic
Acid Pathways Dr. Reyes
Dr. Reyes
August 3, 2013
I.
TRICARBOXYLIC ACID
I. Tricarboxylic Acid
A. Overview of Citric Acid Cycle
B. Pathways
C. Energetics of TCA cycle
D. Summary of TCA cycle
E. Other Aspects of the cycle
F. Catabolism of the Major Nutrients Converge on
G. the TCA cycle
H. Role of Vitamins in TCA cycle
I. Amphibolic Nature of TCA cycle
J. Anaplerotic Reactions
K. Regulation of Krebs cycle
L. Clinical correlation
M. ATP Yields
N. Shuttle Mechanisms for Cytoplasmic Reducing
O. Equivalents
P. Summary of all Reactions of TCA cycle
II. Pyruvate Dehydrogenase Complex
A. General Nature of Pyruvate Dehydrogenase Complex
B. Fate of Pyruvate
C. PDH Complex Mechanism of Action
D. Pyruvate Dehydrogenase Regulation
E. Alterations in PDH Complex
III. Pentose Phosphate Pathway
A. Two Phases of Pentose Phosphate Pathway
B. Differences between Glycolysis and Pentose Phosphate Pathway
C. Biomedical Importance of Pentose Phosphate Pathway
D. Other pathways that require NADPH
IV. Uronic Acid Cycle
V. Appendix
Other names:
A. Krebs Cycle: (after Hans Krebs), biochemist who
discovered the cycle in 1930
B. Tricarboxylic Acid Cycle (TCA): most common
name of the pathway because of the involvement of
tricarboxylates: citrate and isocitrate
Site: Mitochondrion (matrix)
*appropriate location since the 2 primary sources of acetyl
CoA: pyruvate dehydrogenase complex and fatty acid oxidation sequence, are located in the mitochondrion
OBJECTIVES
At the end of the lecture, the student should be able to:
1. Explain the Unique features and their roles in carbohydrate
metabolism: (pyruvate dehydrogenase reaction, TCA cycle,
HMP shunt, Uronic Acid Pathways)
2. Discuss the Regulation of the PDH reaction.
TCA
1.
2.
3.
4.
5.
6.
7.
1.
2.
3.
References:
Carbohydrate Metabolism Lecture Notes by Dr. Reyes
Citric Acid Cycle PPT by Dr. Madarcos
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[Biochem]
CLINICAL CORRELATION
Deficiency in the E1: inability to convert pyruvate to acetyl
CoA pyruvate shunted to lactic acid via lactate
dehydrogenase congenital lactic acidosis problems for
the brain that utilizes ATP from pyruvate oxidation.
2) Synthesis of Citrate from
Oxaloacetate (or Condensation)
Acetyl
CoA
and
10 Steps Pathway
1)
a.
b.
c.
3)
[Biochem]
c.
4)
Dihydrolipoamide dehydrogenase)
a.
a.
b.
5)
b.
a.
[Biochem]
8)
Hydration of Fumarate
a.
9)
b.
c.
d.
e.
Freely reversible
+
FAD is used as a hydrogen acceptor (instead of
+
the more usual NAD )
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[Biochem]
3.
4.
5.
Legend:
Words in Bold end-product per step
Words Underlined enzyme/s used
1.
2.
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[Biochem]
Niacin (NAD )
Thiamine (TPP)
Riboflavin (FAD)
Active Form
Thiamine (B1)
Thiamine
pyrophosphate
(TPP)
Riboflavin (B2)
Flavin adenine
dinucleotide (FAD)
Niacin (B3)
Nicotinamide
adenine dinucleotide
(NAD)
Pantothenic acid
Component of
Coenzyme A
Function
Coenzyme for
decarboxylation in
the pyruvate
dehydrogenase
complex, isocitrate
dehydrogenase & ketoglutarate
dehydrogenase
complex
Cofactor of
succinate
dehydrogenase
Electron acceptor
for isocitrate
dehydrogenase, ketoglutarate
dehydrogenase
complex & malate
dehydrogenase
Cofactor attached to
active carboxylic
acid residues, such
as acetyl-coA and
succinyl coA
Carbohydrate
1.
2.
3.
NITROGEN
METABOLISM:
aspartate
from
oxaloacetate serves as a source of nitrogen in the
production of arginosuccinate and purines; fumarate is
the end product which then enters the TCA cycle
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[Biochem]
5.
HEME SYNTHESIS:
a. Succinyl CoA can be removed from the cycle,
condense with glycine and serve as a precursor of
the porphyrins, biosynthesis of hemes in the liver
and bone marrow, cytochromes and other heme
proteins
b. Succinyl CoA may also be converted to succinate,
a Krebs Cycle intermediate
ANAPLEROTIC REACTIONS
c. Isocitrate dehydrogenase
d. -ketoglutarate dehydrogenase
2. Allosteric control is the main regulatory mechanism.
3. The activity of these enzymes is immediately dependent
on the supply of oxidized dehydrogenase cofactors like
NAD, ADP and ATP and dependent on the energy
status of the cell expressed as [ATP]/[ADP] and
+
[NAHD]/[NAD ] ratio
A. Pyruvate Dehydrogenase
Allosteric inhibitors: ATP, NADH and acetyl CoA or in the
presence of sufficient energy supply of the cell as in a
+
resting state (or [ATP]/[ADP], [NAHD]/[NAD ] and [Acetyl
CoA]/[CoA] ratio.
Acetyl CoA here exerts a product inhibition; it is,
+2
however, activated by Allosteric activator: Ca .
B. Citrate Synthase
Allosteric inhibitors: ATP, NADH, Succinyl CoA, longchain fatty acyl CoA, & citrate (a product inhibitor).
C. Isocitrate Dehydrogenase
Allosteric inhibitors: ATP & NADH
+
+2
Allosteric activators: ADP, NAD & Ca
+2
from contracting heart and other muscle
Ca
tissues released from the ER to provide an
additional activator when ATP is being hydrolysed).
D. -Ketoglutarate Dehydrogenase
Allosteric inhibitors: by ATP, GTP, NADH & succinyl CoA
succinyl CoA exerts a product inhibition or a
product regulates its own synthesis, hence ketoglutarate is available for biosynthetic reactions.
+2
Allosteric activator: Ca .
E.
CLINICAL CORRELATION
[Biochem]
REACTANTS:
+
Acetyl CoA + 3 NAD + 1 GDP + Pi + 2 H2O
REACTION
MECHANISM
ATP YIELD
Isocitrate
NADH, OxPhos
3
dehydrogenase
-ketoglutarate
NADH, OxPhos
3
dehydrogenase
Succinyl CoA
Substrate-level
1
synthase
Phospho.
Succinate
FADH2, OxPhos
2
dehydrogenase
Malate
NADH, OxPhos
3
dehydrogenase
TOTAL
12
PYRUVATE NADH, Oxid. Phospho.
3
*2 pyruvates (glycolysis) oxidized in TCA = 30ATPs
**Oxid. = oxidation; Phospho. = phosphorylation
PRODUCTS:
+
CoA-SH + 3 NADH + 3 H + 1 GTP + 2 CO2
Lipoamide
FAD
Stoichiometric cofactors
CoA
NAD+
Abbr
Prosthetic
groups
Pyruvate
Decaboxylase
E1
TPP
Dihydrolipoyltransacetylase
E2
Lipoamide
Dihydrolipoyl
dehydrogenase
E3
FAD
Action
Oxidative
decarboxylation
of pyruvate
Transfer of
acetyl group to
CoA
Regenerates
oxidized
lipoamide
FATE OF PYRUVATE
A.
2.
3.
B.
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[Biochem]
th
A.
B.
C.
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[Biochem]
(PDH
Step 2:
Step 3:
Overview of the Oxidative Phase of HMP(note the products
formed: NADPH & ribulose-5-PO4)
II. Non-oxidative Phase reversible
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[Biochem]
Substrate: 6-phosphogluconate
Enzyme: 6-phosphogluconate dehydrogenase
Products:
Ribulose-5-PO4
(ketopentose)+
2NADPH + CO2
Form a 6-carbon intermediate, will then become a
5-carbon intermediate
Carbonyl carbon at C2
Step 4:
Substrate: Ribulose-5-PO4
Enzymes: Phosphopentoisomerase
Phosphopentoepimerase
Products: Ribose-5-PO4(aldopentose,
Xylulose-5-PO4(ketopentose)
The isomerase enzyme converts ribulose-5-PO4 to
ribose-5-PO4 while the epimerase enzyme
converts ribulose-5-PO4 to xylulose-5-PO4
Epimerase changes the stereochemical position of
one -OH group at carbon 3
Step 5:
Substrates: Ribose-5-PO4, Xylulose-5-PO4
st
Enzyme:Transketolase (1 )
Products:Sedoheptulose-7-PO4(7 carbon sugar),
Glyceraldehyde-3-PO4
Coenzymes of Transketolase:
1. Thiamine Pyrophosphate/TPP
- important for prolonging RBC lifespan
2. Mg 2+
Transketolase picks up a 2-C fragment from
xylulose-5-PO4 by cleaving the C-C bond between
the keto group and the adjacent carbon thus
releasing glyceraldehyde-3-PO4
The 2-C fragment is covalently bound to thiamine
pyrophosphate, which transfers it to the aldehyde
carbon of another sugar, forming a new ketose
Substrates:Sedoheptulose-7-PO4,
Glyceraldehyde-3-PO4
Enzyme:Transaldolase
Products:Erythrose-4-PO4(4-C sugar)
Fructose-6-PO4(6-C sugar)
Fructose-6-PO4 can be converted to glucose-6PO4 so it serve as an intermediate of the same
pathway; it can also go back to the glycolytic
pathway
The aldol cleavage occurs between the two OH
carbons adjacent to the keto group(on carbons 3
and 4 of sugar)
Step 7:
Substrates: Xylulose-5-PO4, Erythrose-4-PO4
nd
Enzyme: Transketolase (2 )
Products: Glyceraldehyde-3-PO4
Fructose-6-PO4
This step serves as a CONTROL, wherein there is
reversal by the transaldolase and transketolase
enzymes
If
body
needs
more
ribose-5-PO4,
the
transketolase enzyme is the one activated
If body needs more glucose (undergo glycolysis
and gluconeogenesis), the transaldolase enzyme
is the one activated
B. Differences between Glycolysis and Pentose Phosphate
Pathway
Table 4. Table Comparing Glycolysis and PPP
PENTOSE
FEATURES
GLYCOLYSIS
PHOSPHATE
Substrate and
G-6-PO4
Substrate
end product
CO2
Not a product
Product
Hydrogen
+
+
NAD
NADP
Acceptor
ATP Generation
Major function
None
Ribose-5-PO4
None
Present
Generation
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[Biochem]
NADPH
------
Reduced
Hemolytic Anemia
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[Biochem]
L-gulonate
[Biochem]
D-xylulose is phosphorylated at carbon 5 to form Dxylulose 5-phosphate via xylulose kinase further
metabolized via the HMP Shunt converted to
intermediates of glycolysis for energy production.
In essential pentosuria, xylitol dehydrogenase is
absent:
L-xylulose cannot be reduced to xylitol
accumulation of L-xylulosein the blood large
amounts of L-xylulose are seen in the urine of
patients, especially following intake of glucuroniccid.
rare, non-fatal genetic disease.
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[Biochem]
APPENDIX
I.
II.
CoASH
CoA
NAD+
NADH
Source: http://www3.nd.edu/~aseriann/pyrde.html
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[Biochem]